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Volcic M, Nchioua R, Pastorio C, Zech F, Haußmann I, Sauter D, Read C, Walther P, Kirchhoff F. Attenuated replication and damaging effects of SARS-CoV-2 Omicron variants in an intestinal epithelial barrier model. J Med Virol 2024; 96:e29783. [PMID: 38965890 DOI: 10.1002/jmv.29783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
Many COVID-19 patients suffer from gastrointestinal symptoms and impaired intestinal barrier function is thought to play a key role in Long COVID. Despite its importance, the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on intestinal epithelia is poorly understood. To address this, we established an intestinal barrier model integrating epithelial Caco-2 cells, mucus-secreting HT29 cells and Raji cells. This gut epithelial model allows efficient differentiation of Caco-2 cells into microfold-like cells, faithfully mimics intestinal barrier function, and is highly permissive to SARS-CoV-2 infection. Early strains of SARS-CoV-2 and the Delta variant replicated with high efficiency, severely disrupted barrier function, and depleted tight junction proteins, such as claudin-1, occludin, and ZO-1. In comparison, Omicron subvariants also depleted ZO-1 from tight junctions but had fewer damaging effects on mucosal integrity and barrier function. Remdesivir, the fusion inhibitor EK1 and the transmembrane serine protease 2 inhibitor Camostat inhibited SARS-CoV-2 replication and thus epithelial barrier damage, while the Cathepsin inhibitor E64d was ineffective. Our results support that SARS-CoV-2 disrupts intestinal barrier function but further suggest that circulating Omicron variants are less damaging than earlier viral strains.
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Affiliation(s)
- Meta Volcic
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Isabell Haußmann
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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2
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Tang Y, Wu J, Sun X, Tan S, Li W, Yin S, Liu L, Chen Y, Liu Y, Tan Q, Jiang Y, Yang W, Huang W, Weng C, Wu Q, Lu Y, Yuan H, Xiao Q, Chen AF, Xu Q, Billiar TR, Cai J. Cardiolipin oxidized by ROS from complex II acts as a target of gasdermin D to drive mitochondrial pore and heart dysfunction in endotoxemia. Cell Rep 2024; 43:114237. [PMID: 38753484 DOI: 10.1016/j.celrep.2024.114237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Cardiac dysfunction, an early complication of endotoxemia, is the major cause of death in intensive care units. No specific therapy is available at present for this cardiac dysfunction. Here, we show that the N-terminal gasdermin D (GSDMD-N) initiates mitochondrial apoptotic pore and cardiac dysfunction by directly interacting with cardiolipin oxidized by complex II-generated reactive oxygen species (ROS) during endotoxemia. Caspase-4/11 initiates GSDMD-N pores that are subsequently amplified by the upregulation and activation of NLRP3 inflammation through further generation of ROS. GSDMD-N pores form prior to BAX and VDAC1 apoptotic pores and further incorporate into BAX and VDAC1 oligomers within mitochondria membranes to exacerbate the apoptotic process. Our findings identify oxidized cardiolipin as the definitive target of GSDMD-N in mitochondria of cardiomyocytes during endotoxin-induced myocardial dysfunction (EIMD), and modulation of cardiolipin oxidation could be a therapeutic target early in the disease process to prevent EIMD.
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Affiliation(s)
- Yan Tang
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China; Department of Cardiology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Junru Wu
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xuejing Sun
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Shasha Tan
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Wenbo Li
- Department of Plastic and Aesthetic (Burn) Surgery, the Second Xiangya Hospital, Central South University, Changsha 410000, China
| | - Siyu Yin
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Lun Liu
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Yuanyuan Chen
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Yuanyuan Liu
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Qian Tan
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Youxiang Jiang
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Wenjing Yang
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Wei Huang
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Chunyan Weng
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Qing Wu
- Center for High-Performance Computing, Central South University, Changsha 410000, China
| | - Yao Lu
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Hong Yuan
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Qingzhong Xiao
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts, and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Alex F Chen
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China; Department of Cardiology, Institute for Cardiovascular Development and Regenerative Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200092 Shanghai, China
| | - Qingbo Xu
- Department of Cardiology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Jingjing Cai
- Clinical Research Center, Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha 410013, China.
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3
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Giacconi R, D'Aquila P, Cardelli M, Piacenza F, Pierpaoli E, Sena G, Di Rosa M, Bonfigli AR, Galeazzi R, Cherubini A, Fedecostante M, Sarzani R, Di Pentima C, Giordano P, Antonicelli R, Lattanzio F, Passarino G, Provinciali M, Bellizzi D. Blood circulating bacterial DNA in hospitalized old COVID-19 patients. Immun Ageing 2023; 20:76. [PMID: 38111002 PMCID: PMC10726536 DOI: 10.1186/s12979-023-00401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Coronavirus disease COVID-19 is a heterogeneous condition caused by SARS-CoV-2 infection. Generally, it is characterized by interstitial pneumonia that can lead to impaired gas-exchange, acute respiratory failure, and death, although a complex disorder of multi-organ dysfunction has also been described. The pathogenesis is complex, and a variable combination of factors has been described in critically ill patients. COVID-19 is a particular risk for older persons, particularly those with frailty and comorbidities. Blood bacterial DNA has been reported in both physiological and pathological conditions and has been associated with some haematological and laboratory parameters but, to date, no study has characterized it in hospitalized old COVID-19 patients The present study aimed to establish an association between blood bacterial DNA (BB-DNA) and clinical severity in old COVID-19 patients. RESULTS BB-DNA levels were determined, by quantitative real-time PCRs targeting the 16S rRNA gene, in 149 hospitalized older patients (age range 65-99 years) with COVID-19. Clinical data, including symptoms and signs of infection, frailty status, and comorbidities, were assessed. BB-DNA was increased in deceased patients compared to discharged ones, and Cox regression analysis confirmed an association between BB-DNA and in-hospital mortality. Furthermore, BB-DNA was positively associated with the neutrophil count and negatively associated with plasma IFN-alpha. Additionally, BB-DNA was associated with diabetes. CONCLUSIONS The association of BB-DNA with mortality, immune-inflammatory parameters and diabetes in hospitalized COVID-19 patients suggests its potential role as a biomarker of unfavourable outcomes of the disease, thus it could be proposed as a novel prognostic marker in the assessment of acute COVID-19 disease.
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Affiliation(s)
- Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Elisa Pierpaoli
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Giada Sena
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Mirko Di Rosa
- Unit of Geriatric Pharmacoepidemiology and Biostatistics, IRCCS INRCA, Ancona, Italy
| | | | - Roberta Galeazzi
- Clinical Laboratory and Molecular Diagnostic, Italian National Research Center On Aging, IRCCS INRCA, Ancona, Italy
| | - Antonio Cherubini
- Geriatria, Accettazione Geriatrica e Centro Di Ricerca Per L'invecchiamento, IRCCS INRCA, Ancona, Italy
| | - Massimiliano Fedecostante
- Geriatria, Accettazione Geriatrica e Centro Di Ricerca Per L'invecchiamento, IRCCS INRCA, Ancona, Italy
| | - Riccardo Sarzani
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Ancona, Italy, Internal Medicine and Geriatrics, Italian National Research Centre On Aging, Hospital "U. Sestilli", IRCCS INRCA, Ancona, Italy
| | - Chiara Di Pentima
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Ancona, Italy, Internal Medicine and Geriatrics, Italian National Research Centre On Aging, Hospital "U. Sestilli", IRCCS INRCA, Ancona, Italy
| | - Piero Giordano
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Ancona, Italy, Internal Medicine and Geriatrics, Italian National Research Centre On Aging, Hospital "U. Sestilli", IRCCS INRCA, Ancona, Italy
| | | | | | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy.
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4
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Fu L, Baranova A, Cao H, Zhang F. Causal influences of osteoarthritis on COVID-19: a Mendelian randomization study. Front Med (Lausanne) 2023; 10:1287043. [PMID: 38020136 PMCID: PMC10644031 DOI: 10.3389/fmed.2023.1287043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Objective Although observational and genetic studies have indicated a correlation between OA and COVID-19, it remains uncertain whether osteoarthritis (OA) contributes to the severity of COVID-19. Here, we aimed to investigate the potential causal links between the two. Methods In this study, we conducted Mendelian randomization (MR) analysis to investigate whether there is a potential causal connection between OA and COVID-19 outcomes. The analysis utilized publicly available GWAS summary datasets, incorporating data on OA (N = 455,221), SARS-CoV-2 infection (N = 2,597,856), hospitalized COVID-19 (N = 2,095,324), and critical COVID-19 (N = 1,086,211). Additionally, we performed a literature analysis to establish a molecular network connecting OA and COVID-19. Results The MR analysis showed causal effects of OA on hospitalized COVID-19 (OR: 1.21, 95% CI: 1.02-1.43, p = 0.026) and critical COVID-19 (OR: 1.35, 95% CI: 1.09-1.68, p = 0.006) but not on SARS-CoV-2 infection as such (OR: 1.00, 95% CI: 0.92-1.08, p = 0.969). Moreover, the literature-based pathway analysis uncovered a set of specific genes, such as CALCA, ACE, SIRT1, TNF, IL6, CCL2, and others, that were found to mediate the association between OA and COVID-19. Conclusion Our findings indicate that OA elevates the risk of severe COVID-19. Therefore, larger efforts should be made in the prevention of COVID-19 in OA patients.
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Affiliation(s)
- Li Fu
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Manassas, VA, United States
- Research Centre for Medical Genetics, Moscow, Russia
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Fuquan Zhang
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
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5
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for Mining Protein Dysregulation in Patients with COVID-19. J Proteome Res 2023; 22:2847-2859. [PMID: 37555633 DOI: 10.1021/acs.jproteome.3c00092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 still has limited treatment options. Our understanding of the molecular dysregulations that occur in response to infection remains incomplete. We developed a web application COVIDpro (https://www.guomics.com/covidPro/) that includes proteomics data obtained from 41 original studies conducted in 32 hospitals worldwide, involving 3077 patients and covering 19 types of clinical specimens, predominantly plasma and serum. The data set encompasses 53 protein expression matrices, comprising a total of 5434 samples and 14,403 unique proteins. We identified a panel of proteins that exhibit significant dysregulation, enabling the classification of COVID-19 patients into severe and non-severe disease categories. The proteomic signatures achieved promising results in distinguishing severe cases, with a mean area under the curve of 0.87 and accuracy of 0.80 across five independent test sets. COVIDpro serves as a valuable resource for testing hypotheses and exploring potential targets for novel treatments in COVID-19 patients.
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Affiliation(s)
- Fangfei Zhang
- Fudan University, 220 Handan Road, Shanghai 200433, China
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Augustin Luna
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tingting Tan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Yingdan Chen
- Westlake Omics (Hangzhou) Biotechnology Company Limited, Hangzhou, Zhejiang Province 310024, China
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
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6
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Unar A, Bertolino L, Patauner F, Gallo R, Durante-Mangoni E. Pathophysiology of Disseminated Intravascular Coagulation in Sepsis: A Clinically Focused Overview. Cells 2023; 12:2120. [PMID: 37681852 PMCID: PMC10486945 DOI: 10.3390/cells12172120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/12/2023] [Indexed: 09/09/2023] Open
Abstract
Sepsis is a major global health problem that results from a dysregulated and uncontrolled host response to infection, causing organ failure. Despite effective anti-infective therapy and supportive treatments, the mortality rate of sepsis remains high. Approximately 30-80% of patients with sepsis may develop disseminated intravascular coagulation (DIC), which can double the mortality rate. There is currently no definitive treatment approach for sepsis, with etiologic treatment being the cornerstone of therapy for sepsis-associated DIC. Early detection, diagnosis, and treatment are critical factors that impact the prognosis of sepsis-related DIC. Over the past several decades, researchers have made continuous efforts to better understand the mechanisms of DIC in sepsis, as well as improve its quantitative diagnosis and treatment. This article aims to provide a comprehensive overview of the current understanding of sepsis-related DIC, focusing on common causes and diagnoses, with the goal of guiding healthcare providers in the care of patients with sepsis.
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Affiliation(s)
- Ahsanullah Unar
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy; (A.U.); (L.B.); (F.P.); (R.G.)
| | - Lorenzo Bertolino
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy; (A.U.); (L.B.); (F.P.); (R.G.)
| | - Fabian Patauner
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy; (A.U.); (L.B.); (F.P.); (R.G.)
| | - Raffaella Gallo
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy; (A.U.); (L.B.); (F.P.); (R.G.)
| | - Emanuele Durante-Mangoni
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy; (A.U.); (L.B.); (F.P.); (R.G.)
- Unit of Infectious and Transplant Medicine, AORN Ospedali dei Colli-Monaldi Hospital, 80131 Naples, Italy
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7
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Bao D, Xu X, Wang Y, Zhu F, Wu Y, Li H. Clostridium ramosum Bacteremia in an Immunocompetent Patient with SARS-CoV-2 Infection: A Case Report. Infect Drug Resist 2023; 16:4455-4461. [PMID: 37449246 PMCID: PMC10337682 DOI: 10.2147/idr.s421409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023] Open
Abstract
We report a case of Clostridium ramosum bacteremia in a 73-year-old patient with SARS-CoV-2 infection and right lower abdominal tenderness in China. The microbiological features and genomic epidemiological characteristics of C. ramosum worldwide were investigated to identify the possible sources of infection. Whole-genome sequencing of C. ramosum WD-I2 was performed using an Illumina NovaSeq 6000 platform. Phylogenetic analysis of C. ramosum WD-I2 and other publicly available C. ramosum isolates was performed and visualized using the interactive Tree of Life (iTOL) web server. The resistome of C. ramosum WD-I2 consists of two antimicrobial resistance genes (tetM and ermB), which explains the antimicrobial resistance trait to tetracycline and macrolides. Phylogenetic analysis showed that the strain closest to our isolated strain WD-I2 was SUG1069, recovered from a pig feces sample from Canada, which differed by 589 SNPs. To our knowledge, this is the first report of C. ramosum bacteremia in China. Our findings highlight the potential risk of invasive C. ramosum infections during the COVID-19 pandemic.
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Affiliation(s)
- Danni Bao
- Department of Clinical Laboratory, Sanmen People’s Hospital, Taizhou, Zhejiang, People’s Republic of China
| | - Xiaohong Xu
- Department of Clinical Laboratory, Sanmen People’s Hospital, Taizhou, Zhejiang, People’s Republic of China
| | - Yizhang Wang
- Department of Clinical Laboratory, Sanmen People’s Hospital, Taizhou, Zhejiang, People’s Republic of China
| | - Fengjiao Zhu
- Department of Clinical Laboratory, Sanmen People’s Hospital, Taizhou, Zhejiang, People’s Republic of China
| | - Yanhong Wu
- Department of Clinical Laboratory, Sanmen People’s Hospital, Taizhou, Zhejiang, People’s Republic of China
| | - Hongzhang Li
- Department of Gastroenterology, Sanmen People’s Hospital, Taizhou, Zhejiang, People’s Republic of China
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8
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Wang Q, Wang C, Zhang W, Tao Y, Guo J, Liu Y, Liu Z, Liu D, Mei J, Chen F. Identification of biomarkers related to sepsis diagnosis based on bioinformatics and machine learning and experimental verification. Front Immunol 2023; 14:1087691. [PMID: 37449204 PMCID: PMC10337583 DOI: 10.3389/fimmu.2023.1087691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Sepsis is a systemic inflammatory response syndrome caused by bacteria and other pathogenic microorganisms. Every year, approximately 31.5 million patients are diagnosed with sepsis, and approximately 5.3 million patients succumb to the disease. In this study, we identified biomarkers for diagnosing sepsis analyzed the relationships between genes and Immune cells that were differentially expressed in specimens from patients with sepsis compared to normal controls. Finally, We verified its effectiveness through animal experiments. Specifically, we analyzed datasets from four microarrays(GSE11755、GSE12624、GSE28750、GSE48080) that included 106 blood specimens from patients with sepsis and 69 normal human blood samples. SVM-RFE analysis and LASSO regression model were carried out to screen possible markers. The composition of 22 immune cell components in patients with sepsis were also determined using CIBERSORT. The expression level of the biomarkers in Sepsis was examined by the use of qRT-PCR and Western Blot (WB). We identified 50 differentially expressed genes between the cohorts, including 2 significantly upregulated and 48 significantly downregulated genes, and KEGG pathway analysis identified Salmonella infection, human T cell leukemia virus 1 infection, Epstein-Barr virus infection, hepatitis B, lysosome and other pathways that were significantly enriched in blood from patients with sepsis. Ultimately, we identified COMMD9, CSF3R, and NUB1 as genes that could potentially be used as biomarkers to predict sepsis, which we confirmed by ROC analysis. Further, we identified a correlation between the expression of these three genes and immune infiltrate composition. Immune cell infiltration analysis revealed that COMMD9 was correlated with T cells regulatory (Tregs), T cells follicular helper, T cells CD8, et al. CSF3R was correlated with T cells regulatory (Tregs), T cells follicular helper, T cells CD8, et al. NUB1 was correlated with T cells regulatory (Tregs), T cells gamma delta, T cells follicular helper, et al. Taken together, our findings identify potential new diagnostic markers for sepsis that shed light on novel mechanisms of disease pathogenesis and, therefore, may offer opportunities for therapeutic intervention.
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Affiliation(s)
- Qianfei Wang
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Chenxi Wang
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Weichao Zhang
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yulei Tao
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Junli Guo
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yuan Liu
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Zhiliang Liu
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Dong Liu
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Jianqiang Mei
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Fenqiao Chen
- The First Affiliated Hospital ,Hebei University of Chinese Medicine, Shijiazhuang, China
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9
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Qiao H, Morioka Y, Wang D, Liu K, Gao S, Wake H, Ousaka D, Teshigawara K, Mori S, Nishibori M. Protective effects of an anti-4-HNE monoclonal antibody against liver injury and lethality of endotoxemia in mice. Eur J Pharmacol 2023; 950:175702. [PMID: 37059372 DOI: 10.1016/j.ejphar.2023.175702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
4-hydroxy-2-nonenal (4-HNE) is a lipid peroxidation product that is known to be elevated during oxidative stress. During systemic inflammation and endotoxemia, plasma levels of 4-HNE are elevated in response to lipopolysaccharide (LPS) stimulation. 4-HNE is a highly reactive molecule due to its generation of both Schiff bases and Michael adducts with proteins, which may result in modulation of inflammatory signaling pathways. In this study, we report the production of a 4-HNE adduct-specific monoclonal antibody (mAb) and the effectiveness of the intravenous injection of this mAb (1 mg/kg) in ameliorating LPS (10 mg/kg, i.v.)-induced endotoxemia and liver injury in mice. Endotoxic lethality in control mAb-treated group was suppressed by the administration of anti-4-HNE mAb (75 vs. 27%). After LPS injection, we observed a significant increase in the plasma levels of AST, ALT, IL-6, TNF-α and MCP-1, and elevated expressions of IL-6, IL-10 and TNF-α in the liver. All these elevations were inhibited by anti-4-HNE mAb treatment. As to the underlining mechanism, anti-4-HNE mAb inhibited the elevation of plasma high mobility group box-1 (HMGB1) levels, the translocation and release of HMGB1 in the liver and the formation of 4-HNE adducts themselves, suggesting a functional role of extracellular 4-HNE adducts in hypercytokinemia and liver injury associated with HMGB1 mobilization. In summary, this study reveals a novel therapeutic application of anti-4-HNE mAb for endotoxemia.
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Affiliation(s)
- Handong Qiao
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Yuta Morioka
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Dengli Wang
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Keyue Liu
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Shangze Gao
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Hidenori Wake
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Daiki Ousaka
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Kiyoshi Teshigawara
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Shuji Mori
- Department of Pharmacology, Shujitsu University, Okayama, 703-8516, Japan
| | - Masahiro Nishibori
- Department of Translational Research and Drug Development, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan.
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10
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Lin Z. More than a key-the pathological roles of SARS-CoV-2 spike protein in COVID-19 related cardiac injury. SPORTS MEDICINE AND HEALTH SCIENCE 2023:S2666-3376(23)00024-0. [PMID: 37361919 PMCID: PMC10062797 DOI: 10.1016/j.smhs.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 06/28/2023] Open
Abstract
Cardiac injury is common in hospitalized coronavirus disease 2019 (COVID-19) patients and cardiac abnormalities have been observed in a significant number of recovered COVID-19 patients, portending long-term health issues for millions of infected individuals. To better understand how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, CoV-2 for short) damages the heart, it is critical to fully comprehend the biology of CoV-2 encoded proteins, each of which may play multiple pathological roles. For example, CoV-2 spike glycoprotein (CoV-2-S) not only engages angiotensin converting enzyme II (ACE2) to mediate virus infection but also directly activates immune responses. In this work, the goal is to review the known pathological roles of CoV-2-S in the cardiovascular system, thereby shedding lights on the pathogenesis of COVID-19 related cardiac injury.
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Affiliation(s)
- Zhiqiang Lin
- Masonic Medical Research Institute, 2150 Bleecker Street, Utica, NY, 13501, USA
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11
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Tsounis EP, Triantos C, Konstantakis C, Marangos M, Assimakopoulos SF. Intestinal barrier dysfunction as a key driver of severe COVID-19. World J Virol 2023; 12:68-90. [PMID: 37033148 PMCID: PMC10075050 DOI: 10.5501/wjv.v12.i2.68] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 03/21/2023] Open
Abstract
The intestinal lumen harbors a diverse consortium of microorganisms that participate in reciprocal crosstalk with intestinal immune cells and with epithelial and endothelial cells, forming a multi-layered barrier that enables the efficient absorption of nutrients without an excessive influx of pathogens. Despite being a lung-centered disease, severe coronavirus disease 2019 (COVID-19) affects multiple systems, including the gastrointestinal tract and the pertinent gut barrier function. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can inflict either direct cytopathic injury to intestinal epithelial and endothelial cells or indirect immune-mediated damage. Alternatively, SARS-CoV-2 undermines the structural integrity of the barrier by modifying the expression of tight junction proteins. In addition, SARS-CoV-2 induces profound alterations to the intestinal microflora at phylogenetic and metabolomic levels (dysbiosis) that are accompanied by disruption of local immune responses. The ensuing dysregulation of the gut-lung axis impairs the ability of the respiratory immune system to elicit robust and timely responses to restrict viral infection. The intestinal vasculature is vulnerable to SARS-CoV-2-induced endothelial injury, which simultaneously triggers the activation of the innate immune and coagulation systems, a condition referred to as “immunothrombosis” that drives severe thrombotic complications. Finally, increased intestinal permeability allows an aberrant dissemination of bacteria, fungi, and endotoxin into the systemic circulation and contributes, to a certain degree, to the over-exuberant immune responses and hyper-inflammation that dictate the severe form of COVID-19. In this review, we aim to elucidate SARS-CoV-2-mediated effects on gut barrier homeostasis and their implications on the progression of the disease.
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Affiliation(s)
- Efthymios P Tsounis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Christos Konstantakis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Markos Marangos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, Patras 26504, Greece
| | - Stelios F Assimakopoulos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, Patras 26504, Greece
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12
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Eleftheriotis G, Tsounis EP, Aggeletopoulou I, Dousdampanis P, Triantos C, Mouzaki A, Marangos M, Assimakopoulos SF. Alterations in gut immunological barrier in SARS-CoV-2 infection and their prognostic potential. Front Immunol 2023; 14:1129190. [PMID: 37006316 PMCID: PMC10050566 DOI: 10.3389/fimmu.2023.1129190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
Although coronavirus disease 2019 (COVID-19) is primarily associated with mild respiratory symptoms, a subset of patients may develop more complicated disease with systemic complications and multiple organ injury. The gastrointestinal tract may be directly infected by SARS-CoV-2 or secondarily affected by viremia and the release of inflammatory mediators that cause viral entry from the respiratory epithelium. Impaired intestinal barrier function in SARS-CoV-2 infection is a key factor leading to excessive microbial and endotoxin translocation, which triggers a strong systemic immune response and leads to the development of viral sepsis syndrome with severe sequelae. Multiple components of the gut immune system are affected, resulting in a diminished or dysfunctional gut immunological barrier. Antiviral peptides, inflammatory mediators, immune cell chemotaxis, and secretory immunoglobulins are important parameters that are negatively affected in SARS-CoV-2 infection. Mucosal CD4+ and CD8+ T cells, Th17 cells, neutrophils, dendritic cells, and macrophages are activated, and the number of regulatory T cells decreases, promoting an overactivated immune response with increased expression of type I and III interferons and other proinflammatory cytokines. The changes in the immunologic barrier could be promoted in part by a dysbiotic gut microbiota, through commensal-derived signals and metabolites. On the other hand, the proinflammatory intestinal environment could further compromise the integrity of the intestinal epithelium by promoting enterocyte apoptosis and disruption of tight junctions. This review summarizes the changes in the gut immunological barrier during SARS-CoV-2 infection and their prognostic potential.
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Affiliation(s)
- Gerasimos Eleftheriotis
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Efthymios P. Tsounis
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
| | - Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Periklis Dousdampanis
- Department of Renal Diseases, “Agios Andreas” Patras State General Hospital, Patras, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
| | - Athanasia Mouzaki
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Markos Marangos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Stelios F. Assimakopoulos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
- *Correspondence: Stelios F. Assimakopoulos,
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13
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Procalcitonin and Adrenomedullin in Infectious Diseases. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Calcitonin (CT) and adrenomedullin (ADM) are members of the CT family. Procalcitonin (PCT) is a prohormone of CT. Elevations in serum PCT and ADM levels are associated with severe sepsis and coronavirus disease 2019 (COVID-19). PCT enhances sepsis mortality and it binds to the CGRP receptor, which is a heterodimer of CT receptor-like receptor and receptor activity-modifying protein 1. The N-terminal truncated form of PCT, PCT3-116, is produced by the cleavage of PCT by dipeptidyl peptidase 4 (DPP-4) and is the main form of PCT in serum during sepsis, inducing microvascular permeability. Mid-regional pro-adrenomedullin (MR-proADM) is used instead of ADM as a biological indicator because ADM is rapidly degraded, and MR-proADM is released at the same rate as ADM. ADM reduces endothelial permeability and promotes endothelial stability. Endothelial dysfunction is responsible for multiple organ failure in sepsis and COVID-19 patients. Therefore, ADM may be an important molecule for improving the severity associated with sepsis and COVID-19. This review focuses on the current knowledge of PCT and ADM in sepsis and COVID-19.
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14
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COVID-19 Heart Lesions in Children: Clinical, Diagnostic and Immunological Changes. Int J Mol Sci 2023; 24:ijms24021147. [PMID: 36674665 PMCID: PMC9866514 DOI: 10.3390/ijms24021147] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
In the beginning of COVID-19, the proportion of confirmed cases in the pediatric population was relatively small and there was an opinion that children often had a mild or asymptomatic course of infection. Our understanding of the immune response, diagnosis and treatment of COVID-19 is highly oriented towards the adult population. At the same time, despite the fact that COVID-19 in children usually occurs in a mild form, there is an incomplete understanding of the course as an acute infection and its subsequent manifestations such as Long-COVID-19 or Post-COVID-19, PASC in the pediatric population, correlations with comorbidities and immunological changes. In mild COVID-19 in childhood, some authors explain the absence of population decreasing T and B lymphocytes. Regardless of the patient's condition, they can have the second phase, related to the exacerbation of inflammation in the heart tissue even if the viral infection was completely eliminated-post infectious myocarditis. Mechanism of myocardial dysfunction development in MIS-C are not fully understood. It is known that various immunocompetent cells, including both resident inflammatory cells of peripheral tissues (for example macrophages, dendritic cells, resident memory T-lymphocytes and so on) and also circulating in the peripheral blood immune cells play an important role in the immunopathogenesis of myocarditis. It is expected that hyperproduction of interferons and the enhanced cytokine response of T cells 1 and 2 types contribute to dysfunction of the myocardium. However, the role of Th1 in the pathogenesis of myocarditis remains highly controversial. At the same time, the clinical manifestations and mechanisms of damage, including the heart, both against the background and after COVID-19, in children differ from adults. Further studies are needed to evaluate whether transient or persistent cardiac complications are associated with long-term adverse cardiac events.
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15
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Bacorn M, Romero-Soto HN, Levy S, Chen Q, Hourigan SK. The Gut Microbiome of Children during the COVID-19 Pandemic. Microorganisms 2022; 10:microorganisms10122460. [PMID: 36557713 PMCID: PMC9783902 DOI: 10.3390/microorganisms10122460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiome has been shown to play a critical role in maintaining a healthy state. Dysbiosis of the gut microbiome is involved in modulating disease severity and potentially contributes to long-term outcomes in adults with COVID-19. Due to children having a significantly lower risk of severe illness and limited sample availability, much less is known about the role of the gut microbiome in children with COVID-19. It is well recognized that the developing gut microbiome of children differs from that of adults, but it is unclear if this difference contributes to the different clinical presentations and complications. In this review, we discuss the current knowledge of the gut microbiome in children with COVID-19, with gut microbiome dysbiosis being found in pediatric COVID-19 but specific taxa change often differing from those described in adults. Additionally, we discuss possible mechanisms of how the gut microbiome may mediate the presentation and complications of COVID-19 in children and the potential role for microbial therapeutics.
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16
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Wang YF, Liang FM, Liu M, Ding LC, Hui JJ, Xu HY, Liu LJ. Is compromised intestinal barrier integrity responsible for the poor prognosis in critically ill patients with pre-existing hyperglycemia? Diabetol Metab Syndr 2022; 14:172. [PMID: 36397109 PMCID: PMC9669527 DOI: 10.1186/s13098-022-00943-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Compromised intestinal barrier integrity can be independently driven by hyperglycemia, and both hyperglycemia and intestinal barrier injury are associated with poor prognosis in critical illness. This study investigated the intestinal barrier biomarkers in critically ill patients, to explore the role of compromised intestinal barrier integrity on the prognosis of critically ill patients with pre-existing hyperglycemia. METHODS This was a retrospective observational study. The relationships between intestinal barrier biomarkers and glycated hemoglobin A1c (HbA1c), fasting blood glucose (FBG), indicators of clinical characteristics, disease severity, and prognosis in critically ill patients were investigated. Then the metrics mentioned above were compared between survivors and non-survivors, the risk factors of 90-day mortality were investigated by logistic regression analysis. Further, patients were divided into HbA1c < 6.5% Group and HbA1c ≥ 6.5% Group, metrics mentioned above were compared between these two groups. RESULTS A total of 109 patients with critical illness were included in the study. D-lactate and lipopolysaccharide (LPS) were associated with sequential organ failure assessment (SOFA) score and 90-day mortality. LPS was an independent risk factor of 90-day mortality. DAO, NEU (neutrophil) proportion, temperature, lactate were lower in HbA1c ≥ 6.5% Group while D-lactate, LPS, indicators of disease severity and prognosis showed no statistical difference between HbA1c < 6.5% Group and HbA1c ≥ 6.5% Group. CONCLUSIONS Intestinal barrier integrity is associated with the disease severity and prognosis in critical illness. Compromised intestinal barrier integrity might be responsible for the poor prognosis in critically ill patients with pre-existing hyperglycemia.
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Affiliation(s)
- Yi-Feng Wang
- Department of Critical Care Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
- Department of Emergency and Critical Care Medicine, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Feng-Ming Liang
- Department of Critical Care Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Min Liu
- Department of Critical Care Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Li-Cheng Ding
- Department of Emergency Medicine, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jiao-Jie Hui
- Department of Critical Care Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Hong-Yang Xu
- Department of Critical Care Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China.
| | - Li-Jun Liu
- Department of Emergency and Critical Care Medicine, Second Affiliated Hospital of Soochow University, Suzhou, China.
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for mining protein dysregulation in patients with COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509819. [PMID: 36203550 PMCID: PMC9536031 DOI: 10.1101/2022.09.27.509819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has limited treatment options partially due to our incomplete understanding of the molecular dysregulations of the COVID-19 patients. We aimed to generate a repository and data analysis tools to examine the modulated proteins underlying COVID-19 patients for the discovery of potential therapeutic targets and diagnostic biomarkers. Methods We built a web server containing proteomic expression data from COVID-19 patients with a toolset for user-friendly data analysis and visualization. The web resource covers expert-curated proteomic data from COVID-19 patients published before May 2022. The data were collected from ProteomeXchange and from select publications via PubMed searches and aggregated into a comprehensive dataset. Protein expression by disease subgroups across projects was compared by examining differentially expressed proteins. We also visualize differentially expressed pathways and proteins. Moreover, circulating proteins that differentiated severe cases were nominated as predictive biomarkers. Findings We built and maintain a web server COVIDpro ( https://www.guomics.com/covidPro/ ) containing proteomics data generated by 41 original studies from 32 hospitals worldwide, with data from 3077 patients covering 19 types of clinical specimens, the majority from plasma and sera. 53 protein expression matrices were collected, for a total of 5434 samples and 14,403 unique proteins. Our analyses showed that the lipopolysaccharide-binding protein, as identified in the majority of the studies, was highly expressed in the blood samples of patients with severe disease. A panel of significantly dysregulated proteins was identified to separate patients with severe disease from non-severe disease. Classification of severe disease based on these proteomic signatures on five test sets reached a mean AUC of 0.87 and ACC of 0.80. Interpretation COVIDpro is an online database with an integrated analysis toolkit. It is a unique and valuable resource for testing hypotheses and identifying proteins or pathways that could be targeted by new treatments of COVID-19 patients. Funding National Key R&D Program of China: Key PDPM technologies (2021YFA1301602, 2021YFA1301601, 2021YFA1301603), Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (LR19C050001), Hangzhou Agriculture and Society Advancement Program (20190101A04), National Natural Science Foundation of China (81972492) and National Science Fund for Young Scholars (21904107), National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS-P41 GM103504). Research in context Evidence before this study: Although an increasing number of therapies against COVID-19 are being developed, they are still insufficient, especially with the rise of new variants of concern. This is partially due to our incomplete understanding of the disease’s mechanisms. As data have been collected worldwide, several questions are now worth addressing via meta-analyses. Most COVID-19 drugs function by targeting or affecting proteins. Effectiveness and resistance to therapeutics can be effectively assessed via protein measurements. Empowered by mass spectrometry-based proteomics, protein expression has been characterized in a variety of patient specimens, including body fluids (e.g., serum, plasma, urea) and tissue (i.e., formalin-fixed and paraffin-embedded (FFPE)). We expert-curated proteomic expression data from COVID-19 patients published before May 2022, from the largest proteomic data repository ProteomeXhange as well as from literature search engines. Using this resource, a COVID-19 proteome meta-analysis could provide useful insights into the mechanisms of the disease and identify new potential drug targets.Added value of this study: We integrated many published datasets from patients with COVID-19 from 11 nations, with over 3000 patients and more than 5434 proteome measurements. We collected these datasets in an online database, and generated a toolbox to easily explore, analyze, and visualize the data. Next, we used the database and its associated toolbox to identify new proteins of diagnostic and therapeutic value for COVID-19 treatment. In particular, we identified a set of significantly dysregulated proteins for distinguishing severe from non-severe patients using serum samples.Implications of all the available evidence: COVIDpro will support the navigation and analysis of patterns of dysregulated proteins in various COVID-19 clinical specimens for identification and verification of protein biomarkers and potential therapeutic targets.
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